I was thinking about how you can put special set items on your ship and it can effect the look of your ship on the outside but why does it do nothing on the inside.

A good example of this is the Borg set. The outside of your ship looks like you salvaged your ship from the Borg but the inside is no different. You would think that the inside would be full of Borg stuff just like the outside.

Other item sets would give different effects on the interior of your ship.